ProtoMol, an object-oriented framework for prototyping novel algorithms for molecular dynamics

Document Type

Article

Publication Date

9-1-2004

Abstract

PROTOMOL is a high-performance framework in C++ for rapid prototyping of novel algorithms for molecular dynamics and related applications. Its flexibility is achieved primarily through the use of inheritance and design patterns (object-oriented programming). Performance is obtained by using templates that enable generation of efficient code for sections critical to performance (generic programming). The framework encapsulates important optimizations that can be used by developers, such as parallelism in the force computation. Its design is based on domain analysis of numerical integrators for molecular dynamics (MD) and of fast solvers for the force computation, particularly due to electrostatic interactions. Several new and efficient algorithms are implemented in PROTOMOL. Finally, it is shown that PROTOMOL'S sequential performance is excellent when compared to a leading MD program, and that it scales well for moderate number of processors. Binaries and source codes for Windows, Linux, Solaris, IRIX, HP-UX, and AIX platforms are available under open source license at http://protomol.sourceforge.net.

Identifier

8344261362 (Scopus)

Publication Title

ACM Transactions on Mathematical Software

External Full Text Location

https://doi.org/10.1145/1024074.1024075

ISSN

00983500

First Page

237

Last Page

265

Issue

3

Volume

30

This document is currently not available here.

Share

COinS